Automated and assisted RNA resonance assignment using NMR chemical shift statistics

被引：37

作者：

Aeschbacher, Thomas ^{[1
]}

Schmidt, Elena ^{[2
,3
]}

Blatter, Markus ^{[1
]}

Maris, Christophe ^{[1
]}

Duss, Olivier ^{[1
]}

Allain, Frederic H. -T. ^{[1
]}

Guentert, Peter ^{[2
,3
,4
]}

Schubert, Mario ^{[1
]}

机构：

[1] ETH, Inst Mol Biol & Biophys, CH-8093 Zurich, Switzerland

[2] Ctr Biomol Magnet Resonance, Inst Biophys Chem, D-60438 Frankfurt, Germany

[3] Frankfurt Inst Adv Studies, D-60438 Frankfurt, Germany

[4] Tokyo Metropolitan Univ, Grad Sch Sci & Engn, Hachioji, Tokyo 1920397, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / 18期

基金：

瑞士国家科学基金会; 日本学术振兴会;

关键词：

TORSION ANGLE DYNAMICS; ALGORITHM;

D O I：

10.1093/nar/gkt665

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and H-1 and C-13 chemical shifts. Statistics of resonances from regularly Watson-Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1'/C1' chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92-100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding C-13 resonances, which provides an important step toward automated structure determination of RNAs.

引用

页数：14